Статті в журналах: "Structural kinetic modelling"

1

Aftandiliants, Ye G. "Modelling of structure forming in structural steels." Naukovij žurnal «Tehnìka ta energetika» 11, no. 4 (September 10, 2020): 13–22. http://dx.doi.org/10.31548/machenergy2020.04.013.

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The study showed that the influence of alloying elements on the secondary structure formation of the steels containing from 0.19 to 0.37 wt. % carbon; 0.82-1.82 silicon; 0.63-3.03 manganese; 1.01-3.09 chromium; 0.005-0.031 nitrogen; up to 0.25 wt.% vanadium and austenite grain size is determined by their change in the content of vanadium nitride phase in austenite, its alloying and overheating above tac3, and the dispersion of ferrite-pearlite, martensitic and bainitic structures is determined by austenite grain size and thermal kinetic parameters of phase transformations. Analytical dependencies are defined that describe the experimental data with a probability of 95% and an error of 10% to 18%. An analysis results of studying the structure formation of structural steel during tempering after quenching show that the dispersion and uniformity of the distribution of carbide and nitride phases in ferrite is controlled at complete austenite homogenization by diffusion mobility and the solubility limit of carbon and nitrogen in ferrite, and secondary phase quantity in case of the secondary phase presence in austenite more than 0.04 wt. %. Equations was obtained which, with a probability of 95% and an error of 0.7 to 2.6%, describe the real process.

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2

Liebermeister, Wolfram. "Structural Thermokinetic Modelling." Metabolites 12, no. 5 (May 11, 2022): 434. http://dx.doi.org/10.3390/metabo12050434.

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To translate metabolic networks into dynamic models, the Structural Kinetic Modelling framework (SKM) assumes a given reference state and replaces the reaction elasticities in this state by random numbers. A new variant, called Structural Thermokinetic Modelling (STM), accounts for reversible reactions and thermodynamics. STM relies on a dependence schema in which some basic variables are sampled, fitted to data, or optimised, while all other variables can be easily computed. Correlated elasticities follow from enzyme saturation values and thermodynamic forces, which are physically independent. Probability distributions in the dependence schema define a model ensemble, which allows for probabilistic predictions even if data are scarce. STM highlights the importance of variabilities, dependencies, and covariances of biological variables. By varying network structure, fluxes, thermodynamic forces, regulation, or types of rate laws, the effects of these model features can be assessed. By choosing the basic variables, metabolic networks can be converted into kinetic models with consistent reversible rate laws. Metabolic control coefficients obtained from these models can tell us about metabolic dynamics, including responses and optimal adaptations to perturbations, enzyme synergies and metabolite correlations, as well as metabolic fluctuations arising from chemical noise. To showcase STM, I study metabolic control, metabolic fluctuations, and enzyme synergies, and how they are shaped by thermodynamic forces. Considering thermodynamics can improve predictions of flux control, enzyme synergies, correlated flux and metabolite variations, and the emergence and propagation of metabolic noise.

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3

Korla, Kalyani, and Chanchal K. Mitra. "Kinetic modelling of mitochondrial translation." Journal of Biomolecular Structure and Dynamics 32, no. 10 (September 13, 2013): 1634–50. http://dx.doi.org/10.1080/07391102.2013.833135.

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4

TĂNASE, DOBRE, OANA CRISTINA PÂRVULESCU, and CRISTIAN RĂDUCANU. "Stochastic modelling of polysaccharide hydrolysis." Journal of Engineering Sciences and Innovation 3, no. 1 (January 10, 2018): 25–38. http://dx.doi.org/10.56958/jesi.2018.3.1.25.

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A stochastic model was selected and developed to describe polysaccharide hydrolysis kinetics. This model can accurately predict the hydrolysis kinetics and covers the limitations of some classical kinetic models (e.g., complexity of mathematical models, large number of parameter estimations, change in parameters with a change in hydrolysis conditions, etc.). One of the main advantages of the stochastic mathematical model approach is represented by the fact that the polysaccharide structural characteristics and operating parameters can be separately incorporated into the model. The stochastic process characterizing the model considers that the breakdown of a polysaccharide by hydrolysis is a random process based on the cleavage of a parent macromolecule within a molecular mass range into two descendants within lower molecular mass ranges. The model description and its implementation in the hydrolysis of a hypothetical polysaccharide were presented.

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5

Christensen, F. R., G. Holm Kristensen, and J. la Cour Jansen. "Biofilm Structure – An Important and Neglected Parameter in Waste Water Treatment." Water Science and Technology 21, no. 8-9 (August 1, 1989): 805–14. http://dx.doi.org/10.2166/wst.1989.0283.

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Experimental investigations on the kinetics of wastewater treatment processes in biofilms were performed in a laboratory reactor. Parallel with the kinetic experiments, the influence of the biofilm kinetics on the biofilm structure was studied at macroscopic and microscopic levels. The close interrelationship between biofilm kinetics and structural changes caused by the kinetics is illustrated by several examples. From the study, it is evident that the traditional modelling of wastewater treatment processes in biofilm reactors based on substrate removal kinetics alone will fail in many cases, due to the inevitable changes in the biofilm structure not taken into consideration. Therefore design rules for substrate removal in biofilms used for wastewater treatment must include correlations between the removal kinetics and the structure and development of the biological film.

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6

Huang, P. Y. H., and Y. Ch Fu. "Modelling the kinetics of water loss during deep-fat frying of potato particulates." Czech Journal of Food Sciences 32, No. 6 (November 27, 2014): 585–94. http://dx.doi.org/10.17221/99/2014-cjfs.

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We developed an empirical model to describe the water loss during deep-fat frying. Raw potato particulates were sliced to form cylinders and subjected to the deep-fat frying at isothermal temperatures of 160, 190, and 220°C. The microstructure properties were assessed by Field Emission Scanning Electron Microscope (FESEM). The plot of the water content versus the frying time showed two distinct regions. A first-order kinetic model correlated with the two irreversible serial rate processes, rapid process and slow process, was hypothesised to describe the water loss during frying. The results showed the simultaneous two first-order kinetic models adequately predicted the water loss of potato particulates during isothermal frying. The effect of temperature on the rate constants, k<sub>1</sub> and k<sub>2</sub>, for the two processes was adequately modelled by the Arrhenius relationship. The observations of structural changes on the surface and in the inner section of potato particulates are critical. These physical pieces of evidence support our assumption that the mechanisms of the water loss (two-stage rate processes) before and after the transition time are different.  

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7

Telenius, Jelena, Anders E. Wallin, Michal Straka, Hongbo Zhang, Erika J. Mancini, and Roman Tuma. "RNA Packaging Motor: From Structure to Quantum Mechanical Modelling and Sequential-Stochastic Mechanism." Computational and Mathematical Methods in Medicine 9, no. 3-4 (2008): 351–69. http://dx.doi.org/10.1080/17486700802168502.

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The bacteriophages of theCystoviridaefamily package their single stranded RNA genomic precursors into empty capsid (procapsids) using a hexameric packaging ATPase motor (P4). This molecular motor shares sequence and structural similarity with RecA-like hexameric helicases. A concerted structural, mutational and kinetic analysis helped to define the mechanical reaction coordinate,i.e.the conformational changes associated with RNA translocation. The results also allowed us to propose a possible scheme of coupling between ATP hydrolysis and translocation which requires the cooperative action of three consecutive subunits. Here, we first test this model by preparing hexamers with defined proportions of wild type and mutant subunits and measuring their activity. Then, we develop a stochastic kinetic model which accounts for the catalytic cooperativity of the P4 hexamer. Finally, we use the available structural information to construct a quantum-chemical model of the chemical reaction coordinate and obtain a detailed description of the electron density changes during ATP hydrolysis. The model explains the results of the mutational analyses and yields new insights into the role of several conserved residues within the ATP binding pocket. These hypotheses will guide future experimental work.

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8

Хамидуллина, Зульфия Абударовна, Альбина Сабирьяновна Исмагилова, and Семен Израилевич Спивак. "Determination of the basis for nonlinear parametric functions of chemical reactions." Вычислительные технологии, no. 3 (July 15, 2020): 29–34. http://dx.doi.org/10.25743/ict.2020.25.3.004.

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Настоящая работа посвящена математическому и компьютерному моделированию кинетики сложных химических реакций. Сформулирована и доказана теорема о соответствии структуры механизма сложной химической реакции с матрицей связей. Разработан и автоматизирован алгоритм определения базиса нелинейных параметрических функций. Реализована теоретико-графовая интерпретация механизма сложной химической реакции Mathematical and computer modelling of the kinetics of complex chemical reactions is considered in the present study. It was formulated that the structural mechanism of complex chemical reaction corresponds to the matrix of bonds. The appropriate theorem was proved. A graph and theoretical technique that allows determining the functional dependences of kinetic parameters directly from the graph of the reaction mechanism is developed. Based on the proposed algorithm, a program for determining the basis of nonlinear parametric functions of kinetic parameters is proposed. The program implements a graph and theoretic interpretation of the mechanisms of complex chemical reactions for constructing stationary kinetic models of catalytic reactions. An algorithm for determining the basis of nonlinear parametric functions is developed and automated. A graph and theoretical interpretation of the mechanism of a complex chemical reaction is implemented

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9

Krayovskyy, Volodymyr, Volodymyr Pashkevych, Mariya Rokomanyuk, Petro Haranuk, Volodymyr Romaka, Yuriy Stadnyk, Lyubov Romaka, and Andriy Horyn. "KINETIC AND ENERGETIC PERFORMANCES OF THERMOMETRIC MATERIAL TiCo1-xMnxSb: MODELLING AND EXPERIMENT." Measuring Equipment and Metrology 82, no. 1 (2021): 19–25. http://dx.doi.org/10.23939/istcmtm2021.01.019.

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The results of a complex study of the semiconductor thermometric material TiСo1-xMnxSb, х=0.01–0.10, for the producing of sensitive elements of thermoelectric and electro resistive sensors are presented. Microprobe analysis of the concentration of atoms on the surface of TiСo1-xMnxSb samples established their correspondence to the initial compositions of the charge, and X-ray phase analysis showed the absence of traces of extraneous phases on their diffractograms. The produced structural studies of the thermometric material TiСo1-xMnxSb allow to speak about the ordering of its crystal structure, and the substitution of Co atoms on Mn at the 4c position generate structural defects of acceptor nature. The obtained results testify to the homogeneity of the samples and their suitability for the study of electrokinetic performances and the manufacture of sensitive elements of thermocouples. Modeling of structural, electrokinetic and energetic performances of TiСo1-xMnxSb, х=0.01–0.10, for different variants of spatial arrangement of atoms is performed. To model energetic and kinetic performances, particularly the behavior of the Fermi level, the band gap, the density of states (DOS) distribution was calculated for an ordered variant of the structure in which Co atoms at position 4c are replaced by Mn atoms. Substitution of Co atoms (3d74s2) by Mn (3d54s2) generates structural defects of acceptor nature in the TiСo1-xMnxSb semiconductor (the Mn atom contains fewer 3d- electrons than Co). This, at the lowest concentrations of impurity atoms Mn, leads to the movement of the Fermi level from the conduction band to the depth of the band gap. In a semiconductor with the composition TiCo0.99Mn0.01Sb, the Fermi level is located in the middle of the band gap, indicating its maximum compensation when the concentrations of ionized acceptors and donors are close. At higher concentrations of impurity Mn atoms, the number of generated acceptors will exceed the concentration of donors, and the concentration of free holes will exceed the concentration of electrons. Under these conditions, the Fermi level approach, and then the level of the valence band TiСo1-xMnxSb cross: the dielectric-metal conductivity transition take place. The presence of a high-temperature activation region on the temperature dependence of the resistivity ln(ρ(1/T)) TiСo1‑xMnxSb at the lowest concentration of impurity atoms Mn, х=001, indicates the location of the Fermi level in the band gap of the semiconductor thermopower coefficient α(Т,х) at these temperatures specify its position - at a distance of ~ 6 meV from the level of the conduction band . In this case, electrons are the main carriers of current. The absence of a low-temperature activation region on this dependence indicates the absence of the jumping mechanism conductivity. Negative values of the thermopower coefficient α(Т,х) TiСo0,99Mn0,01Sb at all temperatures, when according to DOS calculations the concentrations of acceptors and donors are close, and the semiconductor is maximally compensated, can be explained by the higher concentration of uncontrolled donors. However, even at higher concentrations of impurity Mn atoms in TiСo0,98Mn0,02Sb, the sign of the thermopower coefficient α(Т,х) remains negative, but the value of resistivity ρ(х,Т) increases rapidly, and the Fermi level deepens into the forbidden zone at a distance of ~ 30 meV. The rapid increase in the values of the resistivity ρ(х,Т) in the region of concentrations х=0.01–0.02 shows that acceptors are generated in the TiСo1-xMnxSb semiconductor when Co atoms are replaced by Mn, which capture free electrons, reducing their concentration. However, negative values of the thermopower coefficient α(Т,х) are evidence that either the semiconductor has a significant concentration of donors, which is greater than the number of introduced acceptors (х=0.02), or the crystal simultaneously generates defects of acceptor and donor nature. The obtained result does not agree with the calculations of the electronic structure of the TiСo1-xMnxSb semiconductor. It is concluded that more complex structural changes occur in the semiconductor than the linear substitution of Co atoms by Mn, which simultaneously generate structural defects of acceptor and donor nature by different mechanisms, but the concentration of donors exceeds the concentration of generated acceptors. Based on a comprehensive study of the electronic structure, kinetic and energetic performances of the thermosensitive material TiСo1-xMnxSb, it is shown that the introduction of impurity Mn atoms into TiCoSb can simultaneously generate in the semiconductor an acceptor zone (substitution of Co atoms for Mn) and donor zones and of different nature. The ratio of the concentrations of ionized acceptors and donors generated in TiСo1-xMnxSb will determine the position of the Fermi level and the mechanisms of electrical conductivity. However, this issue requires additional research, in particular structural and modeling of the electronic structure of a semiconductor solid solution under different conditions of entry into the structure of impurity Mn atoms. The investigated solid solution TiСo1-xMnxSb is a promising thermometric material.

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10

Yang, Qi, Jie Dong, Tongju Xing, Yi Zhang, Yong Guan, Xiaoli Liu, Ye Tian, and Peng Yu. "RANS-Based Modelling of Turbulent Flow in Submarine Pipe Bends: Effect of Computational Mesh and Turbulence Modelling." Journal of Marine Science and Engineering 11, no. 2 (February 3, 2023): 336. http://dx.doi.org/10.3390/jmse11020336.

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Pipe bend is a critical integral component, widely used in slurry pipeline systems involving various engineering applications, including natural gas hydrate production. The aim of this study is to assess the capability of RANS-based CFD models to capture the main features of the turbulent single-phase flow in pipe bends, in view of the future investigation of the hydrate slurry flow in the same geometry. This is different from the available literature in which only a few accounted for the effects of a combination of computational mesh, turbulence model, and near-wall treatment approach. In this study, three types of mesh configuration were adopted to carry out the computations, namely unstructured mesh and two structured meshes with a uniform and nonuniform inflation layer, respectively. To explore the influence of the turbulence model, standard k-ε, low-Reynolds k-ε, and nonlinear eddy viscosity turbulence model were selected to close RANS equations. Pressure coefficient, mean axial velocity, turbulence intensity, secondary flow velocity, and magnitude of secondary flow were regarded as the critical variables to make a comprehensive sensitivity analysis. Predicted results suggest that turbulent kinetic energy is the most sensitive variable to the computational mesh while others tend to stabilize. The largest difference of turbulence kinetic energy was around 26% between unstructured mesh and structured mesh with a nonuniform inflation layer. Additionally, a fully resolved boundary layer can reduce the sensitivity of mesh on turbulent kinetic energy, especially for a nonlinear turbulence model. However, the large gradient and peak value of turbulence intensity near the inner wall of the bend was not captured by the case with a fully resolved boundary layer, compared with that of the wall function used. Furthermore, it has been confirmed that the same rule was detected also for different curvature ratios, Reynolds numbers, and dimensionless wall distance y+.

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11

TUZA, ZOLTÁN ANDRÁS, GÁBOR SZEDERKÉNYI, KATALIN M. HANGOS, ANTONIO A. ALONSO, and JULIO R. BANGA. "COMPUTING ALL SPARSE KINETIC STRUCTURES FOR A LORENZ SYSTEM USING OPTIMIZATION." International Journal of Bifurcation and Chaos 23, no. 08 (August 2013): 1350141. http://dx.doi.org/10.1142/s0218127413501411.

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In this paper, all possible sparse chemical reaction network structures of a classical three-dimensional Lorenz system are computed assuming a given chemical complex set. The original nonkinetic equations are transformed into kinetic form using two different approaches: firstly, using a state-dependent time-rescaling and secondly, by applying the theory of X-factorable systems. Using the notions of core reactions and core complexes, an effective optimization-based computation approach is proposed for the calculation of all structurally different sparse reaction graphs. The resulting structures are briefly analyzed and compared from a structural point of view.

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12

Mecozzi, Maria Giuseppina, C. Bos, and Jilt Sietsma. "3D Cellular Automata Modelling of Solid–state Transformations Relevant in Low–alloy Steel Production." Solid State Phenomena 172-174 (June 2011): 1140–45. http://dx.doi.org/10.4028/www.scientific.net/ssp.172-174.1140.

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A three-dimensional cellular automata (CA) model is developed for the kinetic and microstructural modelling of the relevant metallurgical mechanisms occurring in the annealing stage of low–alloy steels: recrystallisation, pearlite–to–austenite transformation and ferrite–to–austenite transformation on heating and austenite–to–ferrite transformation on cooling. In this model the austenite–to–ferrite transformation is described by a mixed–mode approach, which implies that the transformation kinetics is controlled by both the interface mobility and the diffusivity of the partitioning elements. This approach also allows incorporation of the ferrite nucleation occurring on structural defects. The developed CA algorithm, in which the transformation rules for the grain boundary and interface cells are controlled by the growth kinetics of the forming phase, allows three-dimensional systems to be treated within relatively short simulation times. The simulated microstructure reproduces quite well the microstructure observed in experimental samples. A good agreement is obtained between the experimental and simulated ferrite recrystallisation and ferrite and austenite transformation kinetics. The present approach also models the development of the carbon concentration profile in the austenite, which is, for instance, essential for subsequent martensite formation.

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13

Živanović, Stana, Bintian Lin, Hiep Vu Dang, Sigong Zhang, Mladen Ćosić, Colin Caprani, and Qingwen Zhang. "Evaluation of Inverted-Pendulum-with-Rigid-Legs Walking Locomotion Models for Civil Engineering Applications." Buildings 12, no. 8 (August 11, 2022): 1216. http://dx.doi.org/10.3390/buildings12081216.

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Bipedal models for walkers, originally developed in the research field of biomechanics, have been identified as potential candidates for modelling pedestrians in structural engineering applications. These models provide insight into both the kinetics and kinematics of walking locomotion and are considered to have a significant potential to improve the vibration serviceability assessment of civil engineering structures. Despite this notion, the ability of the bipedal models to represent the key features of the walking gait and natural variability within the pedestrian population are still under-researched. This paper critically evaluates the performance of two bipedal models with rigid legs to realistically both reproduce key features of an individual pedestrian’s walking gait and represent a wide range of individuals. The evaluation is performed for walking on a rigid, rather than vibrating, structure due to the availability of experimental data and expectation that successful modelling on rigid surfaces is a necessary condition for progressing towards modelling on the vibrating structures. Ready-to-use equations are provided and the ability of the models to represent the kinematics and kinetics of individual pedestrians as well as the inter-subject variability typical of the human population is critically evaluated. It was found that the two models could generate realistic combinations of the gait parameters and their correlations, but are less successful in reproducing genuine kinetic and kinematics profiles.

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14

SH. AKHATOV, I., M. M. KHASANOV, and I. G. KHUSAINOV. "AUTO- AND CHAOTIC OSCILLATIONS IN HYDRODYNAMICS OF NON-NEWTONIAN LIQUIDS." International Journal of Bifurcation and Chaos 03, no. 04 (August 1993): 1039–44. http://dx.doi.org/10.1142/s0218127493000854.

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A new approach for the description of the rheological behavior of non-Newtonian liquids (clay solutions, polymer solutions, paraffin containing oil) is developed. By this approach the hydrodynamic phenomena in non-Newtonian liquids depend on the nonlinear kinetics of destruction-reconstruction processes for connecting links between the structural elements of the medium. The mathematical model is based on a respective phenomenological nonlinear kinetic equation. For the description of the nonsteady motion of such liquids between the walls of a rotary viscometer, this equation is supplemented with the equation of motion of the liquid and the equation of motion of the mobile cylinder of the viscometer. A numerical analysis of the dependence of the solutions of this system on the number of revolutions per minute is made. According to this analysis auto- and chaotic oscillations of rotary viscometer readings are the consequence of the joint action of kinetic phenomena in the liquid and inertial properties of the mobile part of the viscometer. The numerical results are qualitatively compared with the experimental data.

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15

Hilditch, Paul, Howard Thomas, and Keith Lucas. "Kinetic implications of structural modification in protein turnover." Biosystems 22, no. 3 (January 1989): 241–48. http://dx.doi.org/10.1016/0303-2647(89)90065-8.

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16

Ye, Jianxiong, Honglei Xu, Xueying Huang, Chongrong Ke, and Enmin Feng. "Dynamics Analysis and Prediction of Genetic Regulation in Glycerol Metabolic Network via Structural Kinetic Modelling." Mathematical Problems in Engineering 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/673120.

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Glycerol can be biologically converted to 1,3-propanediol (1,3-PD) byKlebsiella pneumoniae. In the synthesis pathway of 1,3-PD, the accumulation of an intermediary metabolite 3-hydroxypropionaldehyde (3-HPA) would cause an irreversible cessation of the dynamic system. Genetic manipulation on the key enzymes which control the formation rate and consumption rate of 3-HPA would decrease the accumulation of 3-HPA, resulting in nonlinear regulation on the dynamic system. The interest of this work is to focus on analyzing the influence of 3-HPA inhibition on the stability of the dynamic system. Due to the lack of intracellular knowledge, structural kinetic modelling is applied. On the basis of statistical account of the dynamical capabilities of the system in the parameter space, we conclude that, under weak or no inhibition to the reaction of 3-HPA consumption, the system is much easier to obtain a stable state, whereas strong inhibition to its formation is in favor of stabilizing the system. In addition, the existence of Hopf bifurcation in this system is also verified. The obtained results are helpful for deeply understanding the metabolic and genetic regulations of glycerol fermentation byKlebsiella pneumoniae.

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17

Lo Schiavo, M. "Population kinetic models for social dynamics: Dependence on structural parameters." Computers & Mathematics with Applications 44, no. 8-9 (October 2002): 1129–46. http://dx.doi.org/10.1016/s0898-1221(02)00221-3.

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18

Gámez, L., E. Martínez, J. M. Perlado, P. Cepas, M. J. Caturla, M. Victoria, J. Marian, C. Arévalo, M. Hernández, and D. Gómez. "Kinetic Monte Carlo modelling of neutron irradiation damage in iron." Fusion Engineering and Design 82, no. 15-24 (October 2007): 2666–70. http://dx.doi.org/10.1016/j.fusengdes.2007.04.040.

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19

Verbraeken, Maarten C., Roberto Mennitto, Veselina M. Georgieva, Elliott L. Bruce, Alex G. Greenaway, Paul A. Cox, Jung Gi Min, Suk Bong Hong, Paul A. Wright, and Stefano Brandani. "Understanding CO2 adsorption in a flexible zeolite through a combination of structural, kinetic and modelling techniques." Separation and Purification Technology 256 (February 2021): 117846. http://dx.doi.org/10.1016/j.seppur.2020.117846.

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20

Lee, J. M., M. A. Paesler, D. E. Sayers, and Alain Fontaine. "Kinetic X-ray absorption studies and computer structural modelling of photo-darkening in amorphous arsenic sulfide." Journal of Non-Crystalline Solids 123, no. 1-3 (August 1990): 295–309. http://dx.doi.org/10.1016/0022-3093(90)90799-r.

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21

Grebennikov, Dmitry, Ekaterina Kholodareva, Igor Sazonov, Antonina Karsonova, Andreas Meyerhans, and Gennady Bocharov. "Intracellular Life Cycle Kinetics of SARS-CoV-2 Predicted Using Mathematical Modelling." Viruses 13, no. 9 (August 31, 2021): 1735. http://dx.doi.org/10.3390/v13091735.

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SARS-CoV-2 infection represents a global threat to human health. Various approaches were employed to reveal the pathogenetic mechanisms of COVID-19. Mathematical and computational modelling is a powerful tool to describe and analyze the infection dynamics in relation to a plethora of processes contributing to the observed disease phenotypes. In our study here, we formulate and calibrate a deterministic model of the SARS-CoV-2 life cycle. It provides a kinetic description of the major replication stages of SARS-CoV-2. Sensitivity analysis of the net viral progeny with respect to model parameters enables the identification of the life cycle stages that have the strongest impact on viral replication. These three most influential parameters are (i) degradation rate of positive sense vRNAs in cytoplasm (negative effect), (ii) threshold number of non-structural proteins enhancing vRNA transcription (negative effect), and (iii) translation rate of non-structural proteins (positive effect). The results of our analysis could be used for guiding the search for antiviral drug targets to combat SARS-CoV-2 infection.

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Jivkov, Venelin, Vutko Draganov, and Yana Stoyanova. "Electric Vehicles Mileage Extender Kinetic Energy Storage." Journal of Theoretical and Applied Mechanics 45, no. 1 (March 1, 2015): 17–38. http://dx.doi.org/10.1515/jtam-2015-0002.

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Abstract The proposed paper considers small urban vehicles with electric hybrid propulsion systems. Energy demands are examined on the basis of European drive cycle (NEUDC) and on an energy recuperation coefficient and are formulated for description of cycle energy transfers. Numerical simulation results show real possibilities for increasing in achievable vehicle mileage at the same energy levels of a main energy source - the electric battery. Kinetic energy storage (KES), as proposed to be used as an energy buffer and different structural schemes of the hybrid propulsion system are commented. Minimum energy levels for primary (the electric battery) and secondary (KES) sources are evaluated. A strategy for reduced power flows control is examined, and its impact on achievable vehicle mileage is investigated. Results show an additional increase in simulated mileage at the same initial energy levels.

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23

Pey, Angel L., Tomas Majtan, Jose M. Sanchez-Ruiz та Jan P. Kraus. "Human cystathionine β-synthase (CBS) contains two classes of binding sites for S-adenosylmethionine (SAM): complex regulation of CBS activity and stability by SAM". Biochemical Journal 449, № 1 (7 грудня 2012): 109–21. http://dx.doi.org/10.1042/bj20120731.

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CBS (cystathionine β-synthase) is a multidomain tetrameric enzyme essential in the regulation of homocysteine metabolism, whose activity is enhanced by the allosteric regulator SAM (S-adenosylmethionine). Missense mutations in CBS are the major cause of inherited HCU (homocystinuria). In the present study we apply a novel approach based on a combination of calorimetric methods, functional assays and kinetic modelling to provide structural and energetic insight into the effects of SAM on the stability and activity of WT (wild-type) CBS and seven HCU-causing mutants. We found two sets of SAM-binding sites in the C-terminal regulatory domain with different structural and energetic features: a high affinity set of two sites, probably involved in kinetic stabilization of the regulatory domain, and a low affinity set of four sites, which are involved in the enzyme activation. We show that the regulatory domain displays a low kinetic stability in WT CBS, which is further decreased in many HCU-causing mutants. We propose that the SAM-induced stabilization may play a key role in modulating steady-state levels of WT and mutant CBS in vivo. Our strategy may be valuable for understanding ligand effects on proteins with a complex architecture and their role in human genetic diseases and for the development of novel pharmacological strategies.

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Eriksen, Niels Thomas. "Dynamic modelling of feed assimilation, growth, lipid accumulation, and CO2 production in black soldier fly larvae." PLOS ONE 17, no. 10 (October 26, 2022): e0276605. http://dx.doi.org/10.1371/journal.pone.0276605.

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The black soldier fly (BSF) is becoming a novel farm animal. BSF larvae can be reared on different substrates. Their performance is important but highly variable and different models have been employed to analyze their growth, so far without considering that metabolic rates, growth, and biochemical composition of the larvae are interrelated. This work develops a dynamic model, which describes general growth patterns of BSF larvae and predicts observed variability in larval performances. The model was tested against data from literature, which combines kinetic growth data with measurements of lipid or dry weight content, and CO2 production. The model combines the kinetics of the logistic model with principles from differential energy budget models and considers key events in larval life history, moulting and metamorphosis. Larvae are compartmentised into structural biomass, storage lipids, and a pool of assimilates. Feed assimilation is considered the overall rate limiting process and is reduced in relation to larval weight by a logistic function. A second logistic function further reduces the specific growth rate of structural biomass, causes imbalance between and feed assimilation and growth rates, and leaves a surplus of assimilates to be stored as lipids. Fluxes between compartments consider cost of synthesis of structural biomass and lipids, as well as maintenance. When assimilation falls below maintenance needs, storage lipids are recycled. The model is able to describe growth and lipid contents of BSF larvae reared on chicken feed, growth of feed limited BSF larvae, as well as growth, dry weight content, and CO2 production of BSF larvae reared on different substrate qualities and moisture contents. The model may be used for the analysis of growth and performance of BSF larvae under variable rearing conditions. It can deepen the analyses of experimental data and provide insight into the causes of variability of larval performances.

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25

Glienke, Judith, Michael Stelter, and Patrick Braeutigam. "Degradability of organic micropollutants with sonolysis—Quantification of the structural influence through QSPR modelling." PLOS Water 2, no. 1 (January 30, 2023): e0000082. http://dx.doi.org/10.1371/journal.pwat.0000082.

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Local and climate-driven challenges combined with an increasing anthropogenic pollution of the water compartment all around the world make a sustainable handling of wastewater imperative. New additional treatment methods are under examination, including cavitation-based advanced oxidation processes. To quantify structural influences on chemical processes, quantitative structure-property relationship (QSPR) modelling can be used, which calculates a correlation between a defined endpoint and structural properties expressed by molecular descriptors. In this study, QSPR modelling has been applied to investigate the structural influence on the degradability of organic micropollutants with high-frequency sonolysis. The dataset of a previous study on 32 phenol derivates was expanded by 60 mostly aromatic compounds, whose kinetic degradation constants were obtained in a standardized experimental setup. QSPR modelling was conducted using the software PaDEL for descriptor calculation and QSARINS for the modelling process using a multiple linear regression approach and genetic algorithm. All five OECD-requirements for applicable QSPR models were respected. The obtained model included 12 model descriptors, was evaluated with numerous statistical quality parameters, and shows good regression abilities as well as robustness and predictability (R2 = 0.8651, CCCtr = 0.9277, Q2loo = 0.8010, R2ext = 0.7836, CCCext = 0.8838, Q2F1 = 0.7697). The interpretation of selected model descriptors showed interesting connections between the model results and the experimental background. A strong influence of the polarity of organic compounds on their degradability with high-frequency sonolysis could been quantified, as more nonpolar molecules are degraded faster. Additionally, the impact of specific fingerprints, including for example substituents with heteroatoms, the number of fused and non-fused aromatic rings as well as the numerical appearance of secondary carbon could be identified as relevant for this cavitation-based treatment method.

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26

Baker, A. T., J. A. M. Ramshaw, D. Chan, W. G. Cole та J. F. Bateman. "Changes in collagen stability and folding in lethal perinatal osteogenesis imperfecta. The effect of α1(I)-chain glycine-to-arginine substitutions". Biochemical Journal 261, № 1 (1 липня 1989): 253–57. http://dx.doi.org/10.1042/bj2610253.

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The effect of glycine-to-arginine mutations in the alpha 1 (I)-chain on collagen triple-helix structure in lethal perinatal osteogenesis imperfecta was studied by determination of the helix denaturation temperature and by computerized molecular modelling. Arginine substitutions at glycine residues 391 and 667 resulted in similar small decreases in helix stability. Molecular modelling suggested that the glycine-to-arginine-391 mutant resulted in only a relatively small localized disruption to the helix structure. Thus the glycine-to-arginine substitutions may lead to only a small structural abnormality of the collagen helix, and it is most likely that the over-modification of lysine, poor secretion, increased degradation and other functional sequelae result from a kinetic defect in collagen helix formation resulting from the mutation.

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27

Xu, Jie, Tao Wu, Wei Sun, and Chuang Peng. "Generalization and Modelling of Rigid Polyisocyanurate Foam Reaction Kinetics, Structural Units Effect, and Cell Configuration Mechanism." Cellular Polymers 36, no. 6 (November 2017): 285–312. http://dx.doi.org/10.1177/026248931703600601.

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PIR/PUR ratio was derived from differential manipulation of generalized polyisocyanurate kinetic model. The structural unit effects on polymerization of isocyanurate, urethane and urea linkages were evaluated based on Mayo-Lewise tercopolymerization scheme. The cell microstructural configuration model was further developed from profiled FOAMAT reactivity parameters with integrated analysis of cell interface physics. The interstitial border area was defined by interface free energy theory, the shear viscosity was evaluated by foam motion, gas fraction, and partial pressure, and the cell inflation was re-examined by gas-liquid surface tension variability. The cell anisotropic degree, assumed as an aspect ratio of infinitesimal volume elements in cell uniformity, was characterized by equilibrated work increase of surface energy approximated by 2D stretching deformation from sphere cell to spheroid cell. The relationship between pressure and surface tension of elongated cells was also derived from modelling at the same condition of cell deformation.

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28

Moretti, Laure, Bruno Castanié, Gérard Bernhart, and Philippe Olivier. "Characterization and modelling of cure-dependent properties and strains during composites manufacturing." Journal of Composite Materials 54, no. 22 (March 12, 2020): 3109–24. http://dx.doi.org/10.1177/0021998320912470.

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The geometric stability of structural parts is a critical issue in the aeronautical industry. However, autoclave curing of primary structural composite parts may cause significant distortions and divergences between the mould nominal geometries and the final shapes of the parts. To be able to anticipate such distortions, a robust simulation tool is needed, which can be implemented only if the phenomena involved are properly understood and characterized. The thermo-kinetic behaviour of the M21EV/IMA prepreg is fully characterized in this paper. Thermal strains and chemical shrinkages are measured using Thermo-Mechanical Analysis during the cure and the experimental method developed allows the thermo-chemical strains to be obtained even during the early stages of the cure. An experimental setup is developed to measure the thermo-mechanical behaviour of the material during its cure. Thanks to these measurements, a new constitutive mechanical model, inspired from the CHILE model, is defined. These data are then used as inputs for an FEA simulation of the entire curing process. Finally, the model is validated using the cure degree, glass transition and temperature monitoring, and post-cure distortion measurements.

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29

Pallares Pallares, Andrea, Bram Loosveldt, Solomon N. Karimi, Marc Hendrickx, and Tara Grauwet. "Effect of process-induced common bean hardness on structural properties of in vivo generated boluses and consequences for in vitro starch digestion kinetics." British Journal of Nutrition 122, no. 04 (July 3, 2019): 388–99. http://dx.doi.org/10.1017/s0007114519001624.

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AbstractIn the present study, we evaluated the effect of process-induced common bean hardness on structural properties ofin vivogenerated boluses and the consequences forin vitrostarch digestion. Initially, the impact of human mastication on the particle size distribution (PSD) of oral boluses from common beans with different process-induced hardness levels was investigated through a mastication study. Then the effect of structural properties of selected boluses onin vitrostarch digestion kinetics was assessed. For a particular process-induced hardness level, oral boluses had similar PSD despite differences in masticatory parameters between participants of the mastication study. At different hardness levels, a clear effect of processing (P<0·0001) was observed. However, the effect of mastication behaviour (P=0·1141) was not significant. Two distinctive fractions were present in all boluses. The first one was a cotyledon-rich fraction consisting of majorly small particles (40–125 µm), which could be described as individual cells based on microscopic observations. This fraction increased with a decrease in process-induced hardness. The second fraction (>2000 µm) mostly contained seed coat material and did not change based on hardness levels. Thein vitrostarch digestion kinetics of common bean boluses was only affected by process-induced hardness. After kinetic modelling, significant differences were observed between the reaction rate constant of boluses generated from the hardest beans and those obtained from softer ones. Overall this work demonstrated that thein vitronutritional functionality of common beans is affected to a greater extent by structural properties induced by processing than by mechanical degradation in the mouth.

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30

Haldar, Paramita, and Abhijit Chatterjee. "Seeking kinetic pathways relevant to the structural evolution of metal nanoparticles." Modelling and Simulation in Materials Science and Engineering 23, no. 2 (December 30, 2014): 025002. http://dx.doi.org/10.1088/0965-0393/23/2/025002.

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31

Heirwegh, Karel P. M., Jules A. T. P. Meuwissen, Peter Van den Steen, and Humbert De Smedt. "Modelling of chemical reactions catalysed by membrane-bound enzymes. Determination and significance of the kinetic constants." Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology 995, no. 2 (April 1989): 151–59. http://dx.doi.org/10.1016/0167-4838(89)90074-5.

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32

Chanson, H., Youichi Yasuda, and Iwao Ohtsu. "Flow resistance in skimming flows in stepped spillways and its modelling." Canadian Journal of Civil Engineering 29, no. 6 (December 1, 2002): 809–19. http://dx.doi.org/10.1139/l02-083.

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Dams and weirs must be equipped with adequate flood-release facilities for a safe dissipation of the kinetic energy of the flow. With stepped spillway design, it is essential to accurately predict the flow-resistance contribution of the steps. The authors investigate the flow resistance of skimming flows and associated form losses. Recent laboratory experiments were systematically performed with channel slopes ranging from 5.7° up to 55° and the results are compared with existing laboratory and prototype data. The results provide a better understanding of the basic flow patterns and flow-resistance mechanisms and emphasize that form loss is dominant. Simple analytical models provide a reasonable order of magnitude of the pseudo-boundary shear stress and the recirculation cavity ejection frequency. Altogether, more than 38 model studies and four prototype investigations (for a total of more than 700 data points) are reanalysed.Key words: stepped spillway, flow resistance, skimming flow, form drag, physical and analytical modelling.

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33

Mensah, Anette T., Florence Berne, Sébastien Allard, Sylvie Soreau, and Hervé Gallard. "Kinetic modelling of the bromine-ammonia system: Formation and decomposition of bromamines." Water Research 224 (October 2022): 119058. http://dx.doi.org/10.1016/j.watres.2022.119058.

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34

Lobiak, Alexey, Andrii Plugin, Larisa Kravtsiv, and Oksana Kovalova. "Modelling of motorway bridge spans under modernization with consideration of rheological properties of the materials." MATEC Web of Conferences 234 (2018): 04004. http://dx.doi.org/10.1051/matecconf/201823404004.

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The paper presents a computer modelling technique for modernization of bridgework operations by building-up a mounted reinforced concrete slab. It implements the technique of the evolutionary transformation of a model in one calculation cycle with redistribution of forces between the elements of the built-up section, and consideration of the impact of elastoplastic and rheological properties of the materials. Consideration of the concrete creep implies the application of the generalized kinetic curve of prolonged deformation and phenomenological deformation development equations based on the colloid-chemical concept of the prolonged concrete deformation mechanism. The creep control was implemented through new structural coefficients which determined the structure of matrix interlayers between the sand grains, and mortar between the crushed stone grains. The technique proposed was realized in the program complex “LIRA-SAPR” based on the building information modelling (BIM) and the finite element method (FEM). The multistage modelling technique was shown by an example of calculation of a motorway bridge slab span within the transport structures under modernization along the Lev Landau Avenue in Kharkiv (Ukraine).

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35

SEHRAWAT, Seema, Narayanaswamy SRINIVASAN, and Karumathil P. GOPINATHAN. "Functional characterization and structural modelling of late gene expression factor 4 from Bombyx mori nucleopolyhedrovirus." Biochemical Journal 368, no. 1 (November 15, 2002): 159–69. http://dx.doi.org/10.1042/bj20020456.

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Late gene expression factor 4 (LEF4), a multifunctional protein encoded by the Bombyx mori nucleopolyhedrovirus has been bacterially expressed and characterized. Sequence analyses and three-dimensional modelling of B. mori LEF4 showed that the protein is related to mRNA-capping enzymes, which are organized as two modular domains. Most of the acidic side chains in LEF4 were solvent-exposed and spread all along the fold. A region dominated by negatively charged groups, which protrudes from the larger domain was ideally suited for interactions with proteins having positively charged patches at the surface. The purified LEF4 protein exhibited different enzyme activities associated with mRNA-capping enzymes, i.e. GTP-binding, RNA triphosphatase and guanylate transferase activities. In addition, LEF4 also showed NTP-hydrolysing activity. The kinetic analysis of ATP hydrolysis revealed a sigmoidal response with two deduced binding sites for ATP, whereas the guanylate transferase activity showed a typical hyperbolic response to varying concentrations of GTP with a Km of 330±20μM. Analysis of the modelled three-dimensional structure of LEF4 suggested the presence of crucial residues in sequence motifs important for the integrity of the fold. Mutation of one such conserved and buried tyrosine residue to cysteine in the motif IIIa, located close to the interlobe region of the model, resulted in a 44% loss of guanylate transferase activity of LEF4 but had no effect on the ATPase activity.

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36

Pytela, J., J. Jakeš, and F. Rypáček. "A study of enzymic degradation of a macromolecular substrate, , by gel permeation chromatography and kinetic modelling." International Journal of Biological Macromolecules 16, no. 1 (February 1994): 15–20. http://dx.doi.org/10.1016/0141-8130(94)90005-1.

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37

GARSOUX, Geneviève, Josette LAMOTTE, Charles GERDAY, and Georges FELLER. "Kinetic and structural optimization to catalysis at low temperatures in a psychrophilic cellulase from the Antarctic bacterium Pseudoalteromonas haloplanktis." Biochemical Journal 384, no. 2 (November 23, 2004): 247–53. http://dx.doi.org/10.1042/bj20040325.

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The cold-adapted cellulase CelG has been purified from the culture supernatant of the Antarctic bacterium Pseudoalteromonas haloplanktis and the gene coding for this enzyme has been cloned, sequenced and expressed in Escherichia coli. This cellulase is composed of three structurally and functionally distinct regions: an N-terminal catalytic domain belonging to glycosidase family 5 and a C-terminal cellulose-binding domain belonging to carbohydrate-binding module family 5. The linker of 107 residues connecting both domains is one of the longest found in cellulases, and optimizes substrate accessibility to the catalytic domain by drastically increasing the surface of cellulose available to a bound enzyme molecule. The psychrophilic enzyme is closely related to the cellulase Cel5 from Erwinia chrysanthemi. Both kcat and kcat/Km values at 4 °C for the psychrophilic cellulase are similar to the values for Cel5 at 30–35 °C, suggesting temperature adaptation of the kinetic parameters. The thermodynamic parameters of activation of CelG suggest a heat-labile, relatively disordered active site with low substrate affinity, in agreement with the experimental data. The structure of CelG has been constructed by homology modelling with a molecule of cellotetraose docked into the active site. No structural alteration related to cold-activity can be found in the catalytic cleft, whereas several structural factors in the overall structure can explain the weak thermal stability, suggesting that the loss of stability provides the required active-site mobility at low temperatures.

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38

Korus, Agnieszka, Adam Klimanek, Sławomir Sładek, Andrzej Szlęk, Airy Tilland, Stéphane Bertholin, and Nils Erland L. Haugen. "Kinetic parameters of petroleum coke gasification for modelling chemical-looping combustion systems." Energy 232 (October 2021): 120935. http://dx.doi.org/10.1016/j.energy.2021.120935.

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39

TOPHAM, CHRISTOPHER M., JOHN OVERINGTON, DEVENAND KOWLESSUR, MARK THOMAS, EMRYS W. THOMAS, and KEITH BROCKLEHURST. "Investigation of mechanistic consequences of natural structural variation within the cysteine proteinases by knowledge-based modelling and kinetic methods." Biochemical Society Transactions 18, no. 4 (August 1, 1990): 579–80. http://dx.doi.org/10.1042/bst0180579.

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40

Ramaniuk, O., M. Černý, L. Krásný, and J. Vohradský. "Kinetic modelling and meta-analysis of the B. subtilis SigA regulatory network during spore germination and outgrowth." Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1860, no. 8 (August 2017): 894–904. http://dx.doi.org/10.1016/j.bbagrm.2017.06.003.

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41

Maia, Clarissa G. C., Bárbara C. R. de Araujo, Maria B. de Freitas-Marques, Israel F. da Costa, Maria Irene Yoshida, Wagner da Nova Mussel, Rita de Cássia O. Sebastião, and Júlio S. Rebouças. "Thermal Stability Kinetics and Shelf Life Estimation of the Redox-Active Therapeutic and Mimic of Superoxide Dismutase Enzyme, Mn(III) meso-Tetrakis(N-ethylpyridinium-2-yl)porphyrin Chloride (MnTE-2-PyPCl5, BMX-010)." Oxidative Medicine and Cellular Longevity 2021 (December 6, 2021): 1–12. http://dx.doi.org/10.1155/2021/7003861.

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Mn(III) meso-tetrakis(N-ethylpyridinium-2-yl)porphyrin chloride (MnTE-2-PyPCl5, BMX-010, and AEOL10113) is among the most studied superoxide dismutase (SOD) mimics and redox-active therapeutics, being currently tested as a drug candidate in a phase II clinical trial on atopic dermatitis and itch. The thermal stability of active pharmaceutical ingredients (API) is useful for estimating the expiration date and shelf life of pharmaceutical products under various storage and handling conditions. The thermal decomposition and kinetic parameters of MnTE-2-PyPCl5 were determined by thermogravimetry (TG) under nonisothermal and isothermal conditions. The first thermal degradation pathway affecting Mn-porphyrin structural integrity and, thus, activity and bioavailability was associated with loss of ethyl chloride via N-dealkylation reaction. The thermal stability kinetics of the N-dealkylation process leading to MnTE-2-PyPCl5 decomposition was investigated by using isoconversional models and artificial neural network. The new multilayer perceptron (MLP) artificial neural network approach allowed the simultaneous study of ten solid-state kinetic models and showed that MnTE-2-PyPCl5 degradation is better explained by a combination of various mechanisms, with major contributions from the contraction models R1 and R2. The calculated activation energy values from isothermal and nonisothermal data were about 90 kJ mol–1 on average and agreed with one another. According to the R1 modelling of the isothermal decomposition data, the estimated shelf life value for 10% decomposition ( t 90 % ) of MnTE-2-PyPCl5 at 25°C was approximately 17 years, which is consistent with the high solid-state stability of the compound. These results represent the first study on the solid-state decomposition kinetics of Mn(III) 2-N-alkylpyridylporphyrins, contributing to the development of this class of redox-active therapeutics and SOD mimics and providing supporting data to protocols on purification, handling, storage, formulation, expiration date, and general use of these compounds.

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42

Koch, Michel H. J., Patrice Vachette, and Dmitri I. Svergun. "Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution." Quarterly Reviews of Biophysics 36, no. 2 (May 2003): 147–227. http://dx.doi.org/10.1017/s0033583503003871.

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1. Introduction 1482. Basics of X-ray and neutron scattering 1492.1 Elastic scattering of electromagnetic radiation by a single electron 1492.2 Scattering by assemblies of electrons 1512.3 Anomalous scattering and long wavelengths 1532.4 Neutron scattering 1532.5 Transmission and attenuation 1553. Small-angle scattering from solutions 1563.1 Instrumentation 1563.2 The experimental scattering pattern 1573.3 Basic scattering functions 1593.4 Global structural parameters 1613.4.1 Monodisperse systems 1613.4.2 Polydisperse systems and mixtures 1633.5 Characteristic functions 1644. Modelling 1664.1 Spherical harmonics 1664.2 Shannon sampling 1694.3 Shape determination 1704.3.1 Modelling with few parameters: molecular envelopes 1714.3.2 Modelling with many parameters: bead models 1734.4 Modelling domain structure and missing parts of high-resolution models 1784.5 Computing scattering patterns from atomic models 1844.6 Rigid-body refinement 1875. Applications 1905.1 Contrast variation studies of ribosomes 1905.2 Structural changes and catalytic activity of the allosteric enzyme ATCase 1916. Interactions between molecules in solution 2036.1 Linearizing the problem for moderate interactions: the second virial coefficient 2046.2 Determination of the structure factor 2057. Time-resolved measurements 2118. Conclusions 2159. Acknowledgements 21610. References 216A self-contained presentation of the main concepts and methods for interpretation of X-ray and neutron-scattering patterns of biological macromolecules in solution, including a reminder of the basics of X-ray and neutron scattering and a brief overview of relevant aspects of modern instrumentation, is given. For monodisperse solutions the experimental data yield the scattering intensity of the macromolecules, which depends on the contrast between the solvent and the particles as well as on their shape and internal scattering density fluctuations, and the structure factor, which is related to the interactions between macromolecules. After a brief analysis of the information content of the scattering intensity, the two main approaches for modelling the shape and/or structure of macromolecules and the global minimization schemes used in the calculations are presented. The first approach is based, in its more advanced version, on the spherical harmonics approximation and relies on few parameters, whereas the second one uses bead models with thousands of parameters. Extensions of bead modelling can be used to model domain structure and missing parts in high-resolution structures. Methods for computing the scattering patterns from atomic models including the contribution of the hydration shell are discussed and examples are given, which also illustrate that significant differences sometimes exist between crystal and solution structures. These differences are in some cases explainable in terms of rigid-body motions of parts of the structures. Results of two extensive studies – on ribosomes and on the allosteric protein aspartate transcarbamoylase – illustrate the application of the various methods. The unique bridge between equilibrium structures and thermodynamic or kinetic aspects provided by scattering techniques is illustrated by modelling of intermolecular interactions, including crystallization, based on an analysis of the structure factor and recent time-resolved work on assembly and protein folding.

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43

Sun, Yonggan. "Vibration and Acoustic Radiation of Stiffened Plates Subjected to In-Plane Forces." Advances in Civil Engineering 2022 (April 1, 2022): 1–10. http://dx.doi.org/10.1155/2022/9917664.

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This study is devoted to vibration and acoustic radiation of stiffened plates in the presence of in-plane normal and shear loads using the finite element method. In structural modelling, the plate and stiffeners are treated as separate elements and the strain and kinetic energies of the stiffened plate with an elastic boundary are introduced. The results show good agreement with those obtained using other methods. Parametric studies show that in-plane normal forces have obvious influences on the acoustic radiation efficiency and the sound power level of the structure. Furthermore, the position of in-plane normal forces warrants attention; e.g., the farther the boundary in-plane normal forces from the boundary constraint are, the greater the effect on the acoustic performance is. However, in-plane edge shear loading has little influence on the acoustic performance of structures.

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44

Lynch, N. J., and I. Townsend. "Progress towards an analytical modelling capability for kinetic energy penetrators and complex armours." International Journal of Impact Engineering 29, no. 1-10 (December 2003): 437–47. http://dx.doi.org/10.1016/j.ijimpeng.2003.09.040.

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45

Tuukkanen, Anne T., Alessandro Spilotros, and Dmitri I. Svergun. "Progress in small-angle scattering from biological solutions at high-brilliance synchrotrons." IUCrJ 4, no. 5 (August 8, 2017): 518–28. http://dx.doi.org/10.1107/s2052252517008740.

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Small-angle X-ray scattering (SAXS) is an established technique that provides low-resolution structural information on macromolecular solutions. Recent decades have witnessed significant progress in both experimental facilities and in novel data-analysis approaches, making SAXS a mainstream method for structural biology. The technique is routinely applied to directly reconstruct low-resolution shapes of proteins and to generate atomistic models of macromolecular assemblies using hybrid approaches. Very importantly, SAXS is capable of yielding structural information on systems with size and conformational polydispersity, including highly flexible objects. In addition, utilizing high-flux synchrotron facilities, time-resolved SAXS allows analysis of kinetic processes over time ranges from microseconds to hours. Dedicated bioSAXS beamlines now offer fully automated data-collection and analysis pipelines, where analysis and modelling is conducted on the fly. This enables SAXS to be employed as a high-throughput method to rapidly screen various sample conditions and additives. The growing SAXS user community is supported by developments in data and model archiving and quality criteria. This review illustrates the latest developments in SAXS, in particular highlighting time-resolved applications aimed at flexible and evolving systems.

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46

Tarasov, I. V., S. N. Shevtsov, I. V. Zhilyaev, and E. E. Orozaliev. "Compression Molding Cure Cycle Modelling and Optimization for Large Polymeric Composite Parts Processing." Applied Mechanics and Materials 772 (July 2015): 257–62. http://dx.doi.org/10.4028/www.scientific.net/amm.772.257.

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In order to improve quality and productivity of polymeric composites production we suggest the technique of process simulation and optimization for large parts manufactured by compression molding. Optimal process design includes coupled heat transfer / thermo kinetic cure process formulation, its three-dimensional finite element model (FEM) implementation, its transient analysis at the parameterized thermal control law, and Pareto-based optimization, at which we determine control law parameters ensuring minimum standard deviations of the degree of cure within the cured body. We illustrate this approach via examples of two distinct cases of closed mould design concepts: one for moulds heated in autoclaves by the pressurized heated gas, which acts on the mould surface almost uniformly, and another for moulds with independently controlled built-in electrical heaters such as strip heaters or heated platens that are positioned along the length of the die at locations determined by structural features of the cured part. The suggested approach makes the process design more predictable, easier, faster, and more reliable. It can be adapted to specific manufacturing conditions and allows optimizing tools design and processing conditions before the mould and process control are made.

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47

Redfern, S. A. T. "Mineral transformations." Mineralogical Magazine 64, no. 2 (April 2000): 155–56. http://dx.doi.org/10.1180/002646100549157.

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One of the major goals of mineral science is attaining an understanding of the atomic-scale mechanisms and dynamics of minerals that control their structural transformations as a function of pressure, temperature or chemical composition in the natural environment. Examples of research programmes that sail under this heading include those devoted to observing and modelling the role of phase transformations on controlling mineral microstructures, ordering, elasticity, transport, premelting and exsolution. The geological relevance and intrinsic importance (as being representative of specific properties or thermodynamic/ kinetic behaviour) of mineral transformations has long been appreciated. It prompted the recent initiation of a network on Mineral Transformations (http://www.esc.cam.ac.uk/mintrans/) under the European Union TMR Programme. In response to this development, a special session on Mineral Transformations was held at the EUG congress in Strasbourg last year.

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48

Mwasame, Paul M., Norman J. Wagner, and Antony N. Beris. "On the macroscopic modelling of dilute emulsions under flow." Journal of Fluid Mechanics 831 (October 13, 2017): 433–73. http://dx.doi.org/10.1017/jfm.2017.578.

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A new macroscopic model describing the rheology and microstructure of dilute emulsions with droplet morphology is developed based on an internal contravariant conformation tensor variable which is physically identified with the deformed ellipsoidal geometry of the dispersed phase. The model is consistent with existing first-order capillary number, $O(Ca)$, theory describing the microstructure as well as $O(Ca^{2})$ theory describing the emulsion-contributed extra stress. These asymptotic solutions are also used to determine all of the model parameters, making it the only macroscopic emulsion model that is consistent with all available asymptotic theories in the limit of small $Ca$. The governing equations are obtained from the Poisson and dissipation brackets, as developed for an incompressible fluid system endowed with an internal contravariant second-order tensor, subject to the imposition of the constraint of a unit determinant. First proposed by Maffettone & Minale (J. Non-Newtonian Fluid Mech., vol. 78, 1998, pp. 227–241), this constraint physically corresponds to conservation of the volume of the dispersed phase in the emulsion. The Hamiltonian of the emulsion is expressed through the surface energy of the dispersed phase, in addition to the kinetic energy, following previous work by Grmela et al. (J. Non-Newtonian Fluid Mech., vol. 212, 2014, pp. 1–12), but employing a more accurate evaluation of the surface area in terms of the internal contravariant conformation tensor. Structural predictions of the ellipsoid droplet morphology obtained with the new model are compared with classic experiments by Torza et al. (J. Colloid Interface Sci., vol. 38, 1972, pp. 395–411), showing good agreement.

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Lopes, José Fortes. "Using Different Classic Turbulence Closure Models to Assess Salt and Temperature Modelling in a Lagunar System: A Sensitivity Study." Journal of Marine Science and Engineering 10, no. 11 (November 14, 2022): 1750. http://dx.doi.org/10.3390/jmse10111750.

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Turbulence modelling is an important issue when dealing with hydrodynamic and transport models for better simulation of the transport of dissolved or suspended substances in a body-water. It controls processes involving physical balances (salt and water temperature) and, therefore, the ecosystem equilibrium. The study arises from the need to model the turbulence more efficiently when dealing with extreme situations on the Ria de Aveiro (Portugal), a coastal lagoon shallow water system dominated by tidal transport. Because the turbulence model is coupled to the hydrodynamic and transport models, a correct estimation of the eddy viscosity is important in simulating the salt and the heat transports. The aim is to assess the performance of four turbulence schemes/models (k, k-ε, Smagorinsky’s, and k-ε/Smagorinsky’s (k-ε/Sma), where k is turbulent kinetic energy and ε the dissipation rate of the turbulent kinetic energy) associated to a coupled hydrodynamic and transport models to simulate the eddy viscosity, the salinity, and the temperature. Overall, the results point out that among the different models/schemes used, the is the one which provides a more realistic value of the eddy viscosity within the range (1–6) m2 s−1, but most probably (1–3) m2 s−1. The application of the sensitivity analysis to some non-universal k-ε/Sma parameters evidenced significant sensitivity for the eddy viscosity and the salinity and moderate sensitivity for the water temperature. A 100% adjustment of the parameter values relative to the reference, translated into variations within the range of (1, 4) m2 s−1, (0, 13) PSU, and (1, 2.20) °C, for the eddy viscosity, salinity, and water temperature, respectively.

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Sen, Partho, Henri J. Vial, and Ovidiu Radulescu. "Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways." BMC Systems Biology 7, no. 1 (2013): 123. http://dx.doi.org/10.1186/1752-0509-7-123.

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